The way that most linux file systems work you simply cannot do a safe/useful check on a mounted file system. It's not really safe, and because the system is in use, it can be unreliable. Sadly, sometimes, you have to live with things the way they are until someone does it better ;). Ext4 probably won't pick up this feature (maybe ext5? if it ever happens) but I believe btrfs will, and if it does, you will be able to switch your partitions over when the time comes.

So the best way is boot from SD card , make sure you have e2fsprogs package installed in it..

then run fsck.ext3 /dev/mmcblk1 check which device you want to check/fix.